Mass Effect - Aftermath
by Daknit
Summary: Picks up from the end of ME3, a story about losing everything and trying to rebuild in the strange new future where the distinction between man and machine is naught.
1. Chapter 1

**A/N:** Hello and welcome. This is one of my older ideas when I heard Mass Effect 3 was to be the end of the story. I realized there is alot left, especially in the initial aftermath. This story will continue the character options I picked in game (Femshep, paragon path, reapers defeated with best ending on Synthesis, romanced Liara from the first game and didn't stray from it during 2.)

Oh. Some DLC content is expected to be included, mostly Javik.

This is my first fic, please be gentle :).

Klaxons blared in the Combat Information Center of the Normandy. The galaxy hologram in the center of the room has been zoomed in to show the ship's current progress through the relay and the large wave quickly closing on the small orange triangle indicating the Normandy's position.

Garrus watched the approaching wave from the Commander's position at the base of the holo-display as he listened to the reports coming in around him.

"Anomaly distance 150,000 kilometers and closing."

"Engine output is at maximum, estimate 3 minutes to exit relay."

Three minutes. The wave would hit them in half that time. Garrus shook his head and spoke, his gravelly voice cutting through the noise of the CIC.

"We wont be out before it hits. Full power to aft barriers." Garrus reached over and flipped one scaled finger over the intercom switch, "Tali, we have less than 90 seconds before that wave hits, you have anything left in those engines?"

Tali'Zorah frowned from the engine room, her containment suit obscuring the gesture behind her mask as her gloved fingers worked the controls. "You've got everything we have Garrus, if I try to draw any more power from the engines the Mass Effect generator might overload."

Tali's filtered voice floated through the intercom and Garrus winced at the assessment. He looked around the CIC, his eyes locking with Kaiden, who gave an almost imperceptive nod when their eyes met. No choice then. Garrus took a breath before he spoke towards the speaker, "Tali, we'll be crushed when that wave hits us, do whatever you can, we have to make it to the relay." He reached over and flipped the switch off before whispering to himself, "Or die trying."

Tali blinked in surprise as the order came down. She looked over at Engineer Adams, the "official" Chief Engineer of the ship. "We need to set the main generators to 150%." Her fingers were already moving over the console, not waiting for a response. "I need you to channel the overload to the engines and watch for any spikes in the Mass Effect field. I'll be too busy maintaining the energy flow." Adams didn't like it. Tali could see in his eyes that he knew how dangerous what they were about to attempt was. He locked eyes with Tali, the only part of her he could see through her mask, and he nodded. "Right." The only word he spoke as he ran over to the main Mass Effect Field Output terminal setting to work.

"Speed 1.37c!" Joker called out from the cockpit, his hands moving over the haptic interface before him as one of the rear displays showed the same image from the CIC holo behind him of the approaching wave front. Joker looked over to his co-pilot, EDI and shook his head, "Looks like we're going to have to cut the honeymoon a bit short." He said. The platform for EDI, an infiltration platform converted for her use after it's capture from Cerberus. Despite the lack of synthetic skin, the mech had the form of a beautiful, if a little intense, woman. The bright silver sheen of her skin and the HUD worn over her eyes the only give away that this was not simply a person in the seat. EDI watched Joker. Her face expressionless and when she spoke, her synthesized voice seemed to come from all around as the message also came through the nearby speaker system. "It will be al-." The voice cut off mid sentience the sound of corrupted audio flooding from the speakers as EDI's movements stopped. Joker looked over in worry but a violent tremor from the ship forced his attention back to the controls.

Tali's voice came through the deck two speakers "Mass effect generators are running at 130%... 133%... 140%..." At this readout the ship shuddered violent, almost as through it was a horse attempting to throw a rider. From further away through the tinny speaker Garrus could hear Adams' voice in the background. "Correcting power flow to engines, directing excess energy spike to port barrier generator three."

"Acknowledged. Generator output at 143% and rising. Joker, stand by, we're going to uncouple the acceleration limiter."

Joker's voice almost immediately came back through the system, "Roger that."

Garrus looked over at the wave, now almost on top of the small orange triangle indicator on the display, "Impact in ten seconds." He called out, then flipping his transmitter to ship wide he informed the crew. "All stations, brace for impact in ten seconds." Flicking the broadcast switch off, he turned back in to the pilot/engineering chatter channel, knowing now that everything was in Tali and Joker's hands.

"Mass effect generators at 150% of rated maximum! Rerouting power to engines in three..."

A voice from the CIC called out, "Impact in 7... 6..."

"Two... one, now Joker!"

Joker didn't need to be told twice. His hand already wrapped around the accelerator lever he slammed it as far forward as it would go, physically holding it in position even as he was thrown back into his seat as the inertia dampeners tried to keep up with the massive power load.

"3.. 2.." The counting stopped as everyone looked towards the nearest display showing their route through the conduit. They were gaining on the wave! They were going to make it!

"Distance to wave is increasing, 5,000 kilometers! 5500!" Someone cried out over the din of cheers that had erupted. Joker's voice cut through the noise as he announced, "Relay in 10 seconds, mark." Seconds later the windows outside showed that they had returned to normal space. The black star speck curtain never looked quite so comforting. As soon as he had the ship through the relay, Joker reached over and activated the autopilot and turned his attention to EDI, who was still sitting in the same position she had been. He touched her shoulder, the cold metal below unresponsive. Joker reached over to the comm and flicked through the channels until he found the Normandy's isolated internal comm circuit and keyed in for EDI, "EDI? Can you hear me?" He asked, as soon as he let his finger off the input command his ears were assaulted with the sound of corrupted audio. He savagely reached over and flicked the switch off in annoyance, an edge of fear starting to creep into his mind. He reached over and started to undo his safety harness with the intent of going to investigate the AI suite when a bright flash drew his attention towards the relay.

The glowing energy orb in the middle had changed color, going from the soft blue glow he usually associated with it to a bright green. Joker only saw it for a moment before the energy seemed to shrink down into a single point, growing brighter before it exploded outwards, pieces of the relay flying in all directions and a wave of energy screaming towards the ship. "Oh shi-." Joker didn't even think as he yelled, "Brace yourselves." Back towards the CIC. The wave slammed into the ship, throwing everyone not belted into a seat hard against the walls, ceilings, and floors. Joker jerked violently in his partially fastened harness, his head managing to get enough reach to interact violently with the wall, leaving only darkness behind.

Liara T'Soni sat at her desk in the modified XO quarters looking over the bank of monitors, all angled to be easily visible from her position. Her bright blue eyes focused on the image on the screens, all joining to form a single image of Shepard. Reaching out one azure hand she trailed a finger along the image's jawline. Her thoughts turned inward as she gazed wistfully at the picture.

 _Liara is standing near a wall, one hand running over the surface, noting the slight indented imperfections. 'This doesn't feel like age damage.' she thought. Making a fist, Liara pressed faintly and rubbed away a thousand year layer of dust and grime, revealing a small image. The figure reminded her of Athame at least in overall style. Strange. Liara unshouldered her duffel bag, reaching inside and pulled out a piece of paper, pencil and a small camera. With that, she set to work documenting her find._

 _Several hours later, Liara was pulled from her drawing by a loud chirp from her omni-tool. Looking down at her wrist she squeezed her fist, causing the holographic haptic interface to appear. She touched several keys and brought up a small video screen appeared showing the entrance to the runes. She expected an animal or rock slide to have set off the proximity alarms but what she saw turned her blood cold. Geth. Springing to her feet, Liara roughly shoving her drawing into the duffel bag. She started tapping her omni-tool to bring up a map of the area. She noted one of her earlier references... A console. Setting off at a run, she headed in that direction._

 _Liara hit the room she had marked earlier at a full spring, skidding herself to a stop at the controls. Her omni-tool informed her that three of the five remote sensors she had set up to track movement were had tripped. That meant the Geth could be here in less than five minutes. Knowing time was short Liara looked over the alien control board in front of her, trying to recall everything she could remember about the Protheans from her years of study. After a moment to consider, Liara reached over and laid her palm on the flat surface, a tingling sensation instantly spreading from her palm. A small smile lit her face as the characters before her shifted from the completely unrecognizable alien script to what looked to her to be a variant form of ancient Asari. Liara tapped the controls in the order that seemed most logical to her._

 _Lines of text filled the holographic display before her before the screen wrapped itself in a green border and the words 'Sequence Initiated.' displayed in bright yellow text. A smile spread across her face as she stepped back from the controls, looking towards the archway that would give access to the rest of the complex, smiling more broadly as a blue energy field appeared before her. Liara took a step back, preparing to leave when suddenly a feeling of weightlessness overcame her. She let out a squeak of surprise as she was lifted from the ground, her arms spread out slightly and another blue energy fiend appeared in a sphere around her. "Oh goddess..." She murmured, wondering just what she was going to do now..._

 _Several hours had passed. While she wasn't sure, she was starting to think that she might have activated the entire security system rather than sealing off the room she was in as intended. And now she was stuck in here. She felt an edge of fear creeping into her mind. How was she going to get out of here? Liara closed her eyes and took a deep breath. Focusing herself she struggled to align her body, trying to feel the flow of energy through her. The air before the console flickered briefly before returning to normal. It was no use, her biotics couldn't reach the console without better alignment of her implants. She was stuck for the time being._

 _Liara had lost all track of time as she hung suspended in her prison. Her mind snapped to alertness and she began taking stock of herself. She was hungry and tired, but otherwise seemed to be fine. The sharp sound of weapons fire drawing her attention. It was coming from far too close. Liara weighed her options. After having been stuck for what felt like weeks but had probably been closer to a day or two. She hadn't been able to sleep and her judgment was already starting to go, clearly shown when she called out, "Hello? Is anyone out there?"_

 _The sound of approaching footsteps reached her as a group of three people approached her. A lithe Quarian wearing a purple environmental suit, a Turian male with a sniper rifle held across his chest and... Liara had to force herself not to gasp as her eyes landed on the slightly smaller frame of a human woman. The woman had flaming red hair cut in a short but still stylish military cut and her bright emerald eyes filled with amusement as she took in the situation before the mask of a professional soldier slipped back into place, "Dr. T'Soni?" she asked, a small smirk returning to her lips at the Asari's affirmative response._

Liara opened her eyes. Looking once more at the image frozen on her monitors. Reaching to the controls, she keyed for a video file which spread across the screens before playing. She watched the replay of her last moment with Shepard after she had been injured in the final push to get to the Citadel. The sound was poor quality as the multitude of weapons fire and explosions from all directions muted everything. Liara tapped several controls and the camera zoomed in, focusing on her upturned face as her eyes were locked with Shepard's. She could read the words on her lips as she spoke them, "I am yours." Her eyes slammed closed as she remembered being loaded into the Normandy and the ship lifting off. She was so geared up on adrenaline and worry that she had to be sedated. When she came around, she had wandered in here and began reminiscing.

The ship rocked violently and Garrus' voice suddenly broke through the intercom, "Attention all hands: The energy output from the Citadel is rising. There's nothing more we can do here. Whatever its going to do looks like it'll happen any moment. We're heading through the Sol relay and heading for the rendezvous point. Relay in two minutes, mark." And with that the intercom fell silent. Liara frowned and keyed up to the CIC.

"Garrus, we can't leave yet. What about Shepard?"

There was a long pause before Garrus spoke back. Clearly he had moved to a more private part of the ship to speak to her. "There isn't anything we can do Liara. If our readings are right the Crucible is channeling enough energy to destroy every ship in the system if it goes off."

"Garrus," She started, an edge of panic creeping into her voice, "We can't just abandon her!"

Another pause. "We don't have a choice. Shepard wouldn't want us to get ourselves killed trying to save her." Garrus' voice softened as he continued, "The docks are all locked down and the entire station is crawling with Reapers. We'd never make it before this thing discharges. I'm sorry."

The intercom clicked off as Garrus disconnected. Liara sat back in disbelief. This couldn't be happening. Not like this. Her gaze landed on the viewport just in time to see Pluto zip past and their destination relay coming into view. Liara closed her eyes, her mind focusing and for just a moment an image formed in her mind. She was looking out over an edge. The surface much to smooth and even to be anything except an artificial construction. A bright cylinder of pale blue light was before her. Her gaze travelled down to the pistol in her hand as she checked the power pack. She was surprised at the state of her arm, covered in scratches and blood small bits of pale skin visible beneath... Liara gasped as she realized that she must be seeing through Shepard's eyes! She looked closer and yes, there on her left hand was the small engagement band Liara had given her. Her throat closed involuntarily as the gaze shifted down to an image of a small boy, the image appeared holographic but she could tell there was something special about this one.

"Its time. Make your choice."

Liara felt Shepard take a deep breath as she ran over the options again. She looked left and right before letting out a sigh. Liara was a bit jarred as she found herself confronted with an image of herself and heard the whisper of, "I'm sorry." The image began moving closer to the edge.

"No..." Liara whispered, though her eyes were closed tears were running freely down her cheeks.

Shepard jumped. As she fell Liara was assaulted with Shepard's memories: chasing Saren down, meeting Tali... And then Liara again saw herself. For the first time Liara saw herself through her bond mates eyes. As she watched nearly every significant encounter between the two played out. As she watched herself swear to being Shepard's for the last time she heard the whisper that broke her heart and the connection 'I love you.' Liara willingly surrendered to the darkness that engulfed her following the violent separation from her love's mind.

 **A/N:** Oops. I only meant to make this 2,000 words and it's pushing 3,000. Ah well. I decided to add the scene with Liara in as most of this story is going to focus on her and I was at about 1200 words... which is pitiful. I'm also doing a replay of ME3 for this story (Oh darn… I have to replay a fun game. The horror!). Please leave a review, liked it, didn't like it, found a typo or miswording, have a suggestion… let me know!


	2. Chapter 2

p class="MsoNormal"strongA/N:/strong Okay... so lets see if we can make sense of all these little pieces I've sprinkled. I did find one change that I had to make that being that I had listed Ashley as being on the bridge originally but forgetting that I decided from the first play through on that... Ashley is kind of a shitty person. IMHO anyways. So yeah, that was corrected. Also for the record I haven't forgotten about James, Dr. Chakwas, or anyone else. They'll show up. Now I just have to figure out how to get the crew back to Earth without a Mass Relay or enough fuel... or a working ship. Hrm... Anyways! ONWARDS!/p  
p class="MsoNormal" /p  
p class="MsoNormal" style="text-align: center;"-/p  
p class="MsoNormal"Jeff "Joker" Moreau came back to conscience with a groan. He felt like every bone in his fragile body had been broken. A scraping sound above him caught his attention as he bit back a cry as the metal above him shifted, pressing down more heavily against his rib cage for a moment before the pressure eased off and light flooded onto his face. Joker blinded several times until the world came back into some semblance of order. His eyes landed on the concerned face of EDI's mech. She reached a hand down and offered it to Joker, who grudgingly let himself be pulled up, this time unable to stop a sharp cry of pain as the droid pulled on his arm. Once he was standing, leaning very heavily into EDI he looked around at the state of the ship, suddenly feeling like someone had reached into his chest and twisted his heart around./p  
p class="MsoNormal" /p  
p class="MsoNormal"The bridge of the Normandy was completely destroyed. Sunlight shone through where the windows had been and while the pilot's seat was more or less intact, this section of the ship seemed to have separated itself from the rest as a huge hole in the back of the cockpit looked out onto what appeared to be a forest. Jeff blinked, a small whirring noise making him frown and tense slightly before suddenly his vision seemed to zoom in and he could quite clearly make out the rest of the crew slowly starting to exit what was left of the Normandy./p  
p class="MsoNormal" /p  
p class="MsoNormal""Are you alright, Jeff?" EDI asked. Though her voice still sounded like a computer program drawing on a list of sounds to speak, there was a certain concern and compassion that came through that was definitely new./p  
p class="MsoNormal" /p  
p class="MsoNormal""I'm alive, I have a feeling alright is going to take a while." And a friendly Alliance ship./p  
p class="MsoNormal" /p  
p class="MsoNormal""Can you walk?" She inquired, looking over as Jeff took a tentative step away from EDI. As soon as he attempted to put weight on his leg it buckled, sending him to the ground and causing a sickening crack to echo out from his arm. EDI reached down and slowly maneuvered Jeff into her arms before heading back towards the rest of the ship with him./p  
p class="MsoNormal" /p  
p class="MsoNormal"The ship hadn't fared well. Pieces of it were spread over at least a kilometer or more, the main body had survived intact but the overloading of the Mass Effect generators hadn't been bled off in time before the impact and the resulting differential had caused the engines to quite literally punch themselves out of the ship. The metal from the hull was warped out from the explosion and long cuts were clearly visible allowing atmosphere from outside in./p  
p class="MsoNormal" /p  
p class="MsoNormal""Thank the stars this planet has air." Garrus muttered to himself, glancing around at their surroundings once more. The vegetation around them led him to believe that they wouldn't starve. Well... most of them wouldn't starve. The real challenge would be finding something for himself and Tali to eat. As if summoned by his thoughts, Tali appeared exiting the ship and after a brief look around, headed in Garrus' direction./p  
p class="MsoNormal" /p  
p class="MsoNormal""Report?" He asked, looking at the small woman before him./p  
p class="MsoNormal" /p  
p class="MsoNormal""The ship mostly survived the impact, the engines are gone, I'm guessing they are up in orbit somewhere. Deck 5 and deck 4 were completely smashed together on impact. If we hadn't evacuated the room before the crash we'd be dead..." She paused as the reality of what she said hit her, her eyes, the only thing really visible through her helmet widened before she visibly pulled herself together to continue, "The Tantalus drive will never work again. Most of the forward batteries were destroyed and the cyclonic barriers overloaded when the wave hit us which is what caused the plasma network to overload." Tali waved a hand towards the small section of the rear of the ship which small flickers of flame could be seen. "It's contained for now and Adams is working on bleeding off the plasma to get them out. Deck 3 and up seem mostly in tact." She shook her head, "Of course that's only if you ignore the damage to the hull and structural integrity fields."/p  
p class="MsoNormal" /p  
p class="MsoNormal"Garrus sighed. He knew it would be bad, he'd expected it... but to hear it laid out in front of him. "Obviously the AI core survived." Garrus started and then raised an eyebrow as Tali shook her head./p  
p class="MsoNormal" /p  
p class="MsoNormal""It didn't." She said, her voice quite. "The port side engine cut right through that room on it's way out of the ship. All the computer systems were destroyed."/p  
p class="MsoNormal" /p  
p class="MsoNormal""But then... how...?" Garrus started./p  
p class="MsoNormal" /p  
p class="MsoNormal""I don't know..." She said, looking towards the ship. Though they couldn't see her, they knew that EDI was inside somewhere. "We'll have to ask her." Tali cleared her throat, "Liara and James are in the infirmary, but Dr. Chakwas says they are going to be fine. Steve was up on the observation level during the crash and managed to get away with a couple of cuts and a broken arm. Kaiden has a bad concussion but they're keeping an eye on him." She paused and though it couldn't really be seen, Garrus knew she was offering a smile, "The medical supplies survived, as did most of the contents of cargo bay three."/p  
p class="MsoNormal" /p  
p class="MsoNormal"Garrus smiled softly, "Well, at least we wont starve in our first week, that's something. Thanks Tali." He said, looking back towards the ship, "I guess I should get in there and see it for myself." He said, the weight of the task heavy on his voice as he started that direction. Tali watched him walk away, wanting to help, but knowing that this was something Garrus had to do for himself./p  
p class="MsoNormal" /p  
p class="MsoNormal"A soft thumping sound preceded Garrus as he walked through the hole in the front of the ship where the cockpit had once been attached, looking straight back into what was left of the CIC. "What a mess." He muttered to himself. Support beams had fallen from the ceiling and console had literally been ripped from the wall by the impact. The holodisplay in the center of the room was off, a large crack running down the projector lens down below. Glancing briefly around the room, Garrus headed to the war room first. As he stepped through the door where the weapon scanners were located his eyes fell on a chalk line on the ground, outlining where one of the guards in this room had died in the impact. He shook his head slowly. There would be more. As he walked back he was pleased to see that at least this room had survived mostly intact. Granted the monitors were shattered and the door to the ship board QEC was jammed at an awkward angle but aside from that./p  
p class="MsoNormal" /p  
p class="MsoNormal"Crossing the room, Garrus managed to get his clawed hands between the gap at the lower part of the door. He pulled and the door creaked but didn't budge. Planting his feet Garrus pulled harder and with a loud squeal of metal scraping metal the doors rebounded onto their tracks and shoved aside. Garrus looked into the room and shook his head. Half of it had been caved in, it looked like one of the loose engines had ricocheted off the hull outside this room. Garrus stepped further into the room, looking closer at the actual QEC device. It looked largely intact. Though the main holo-projector in the room was damaged apparently beyond repair, that projector just isolated and focused the image anyways. True without it there wouldn't be any visual link, but at least maybe they would be able to get something on audio at some point. He made a mental note to add it to the list of things that needed to be done before heading to the backup stairwell to deck three./p  
p class="MsoNormal" /p  
p class="MsoNormal"The interior of the ship was almost solid black, only the glow lamps set up along the hallways allowed anyone to move from one spot to another without risking broken limbs. Garrus headed towards the medical bay, pausing outside the door as he let his eyes adjust. Though power throughout the ship was gone, Tali and Dr. Chakwas had managed to dig up some temporary power cells. They wouldn't last long, maybe a week if they were only running this room, but at least for now... Garrus looked at the four people occupying the room, two in beds, one at a nearby computer terminal looking over the reports flowing by on the screen and the last standing near one of the beds, gazing down at it's occupant with worry etched on her features./p  
p class="MsoNormal" /p  
p class="MsoNormal"Garrus made his way over to Dr. Chakwas who was looking over Joker's medical files. He placed one hand on the back of her chair, alerting her to his presence. "How's it looking Doc?" He asked, not entirely sure he wanted to hear the answer./p  
p class="MsoNormal" /p  
p class="MsoNormal""Surprisingly well. I expected Jeff would have broken every bone in his body on impact. If it wasn't for a split along his shin bone, I'd say he could leave right now." She motioned to the computers, "It's unprecedented. With Jeff's Vrolik syndrome I would have expected to tell you that he'd never walk or fly a ship again." She shook her head and looked over at her charge, "I'm running tests now to try and determine the cause."/p  
p class="MsoNormal" /p  
p class="MsoNormal"Garrus nodded, "Thanks Doc. Keep me informed." Garrus walked over closer to the person in the other bed. Liara's soft blue features were visible up to about her neck where a blanket covered the rest of her. "And her?" Garrus inquired./p  
p class="MsoNormal" /p  
p class="MsoNormal"Dr. Chakwas shook her head, "Still unconscious. But I can't find any sign of injury to the head or neck, no signs of trauma. Not even a bruise. I'm running tests on her as well." Garrus frowned, this was very strange. He shook his head slowly and then glanced at the room's other occupant. EDI. "EDI, lets take a walk." Garrus said. EDI looked up as he spoke, her eyes narrowed briefly before turning towards Jeff. "Yes... I suppose we should." Her eyes glanced over at the AI core behind the door to her right. She knew everything in there had been destroyed. When the engines broke free the room had been exposed to space and the automatic atmosphere containment system had closed the emergency bulkheads. Unfortunately, the violent shaking of the computers resulted in EDI's primary processors ending up directly under the door and being smashed. Yes, there would be questions, no doubt about it./p  
p class="MsoNormal" /p  
p class="MsoNormal"strongA/N:/strong Okay, I dunno how long this is but I'm calling a stop here because getting in to the whole stuff with EDI is going to require a section on it's own mostly. I hope you're enjoying, I know it's slow but I'm not in any hurry and am just telling what I see as I see it. Let me know if you like or don't like or have any suggestions or criticisms. Thanks for stopping by!/p 


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